Velmeshev_et_al.1 CELLxGENE Census 2024-07-01 cutoff 0 MADs 5

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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.28

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Velmeshev_et_al.1 CELLxGENE Census 2024-07-01 cutoff 0 MADs 5

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the PavlidisLab/sc-annotation-pipeline analysis pipeline.
        Report generated on 2025-07-25, 14:35 PDT based on data in: /space/grp/rschwartz/rschwartz/cell_annotation_cortex.nf/work/98/915d17c7b8907a5b8b6ea8aa2fa9bb/Velmeshev_et_al.1

        Sample cell type composition

        Composition per sample of predicted cell types.

        Created with MultiQC

        Leiden cluster composition (cell types)

        Leiden clustering performed on log-transformed data with top 2000 variable genes, 10 PCs, 30 neighbors, resolution = 0.3.

        Created with MultiQC

        Cell type markers

        Expression of select markers. Count are averaged across cell-type labels and z-score normalized across genes.

        Created with MultiQC

        Cell type UMAP

        UMAP of the cell type labels, sample names and leiden clusters.

        Velmeshev et al 1 | 5144 PFC Nova upset

        Velmeshev et al 1 | 5144 PFC Nova outliers

        Velmeshev et al 1 | 5936 PFC Nova outliers

        Velmeshev et al 1 | 5945 PFC Nova upset

        Velmeshev et al 1 | 5893 PFC Nova upset

        Velmeshev et al 1 | 5408 PFC Nova outliers

        Velmeshev et al 1 | 5936 PFC Nova upset

        Velmeshev et al 1 | 5879 PFC Nova outliers

        Velmeshev et al 1 | 5419 PFC upset

        Velmeshev et al 1 | 5879 PFC Nova upset

        Velmeshev et al 1 | 5403 PFC Nova outliers

        Velmeshev et al 1 | 5419 PFC outliers

        Velmeshev et al 1 | 5408 PFC Nova upset

        Velmeshev et al 1 | 5403 PFC Nova upset

        Velmeshev et al 1 | 5945 PFC Nova outliers

        Velmeshev et al 1 | 5893 PFC Nova outliers

        Velmeshev et al 1 | 5278 PFC Nova upset

        Velmeshev et al 1 | 5538 PFC Nova outliers

        Velmeshev et al 1 | 5278 PFC Nova outliers

        Velmeshev et al 1 | 5538 PFC Nova upset

        MultiQC v1.28 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.